Yelm huh, that's a trek...
If the egr valve is stuck open or in the open position constantly letting the exhaust gasses feed into the compressor, I'd say yes, it's bad to run it like that, the system is designed to recirculate those gasses intermittently tho. iirc the egr valve closes when the truck is shut off and if it's tuned for a blocker/delete the valve should be and stay shut, so it "shouldn't" be to big of an issue although the valve doesn't seal off perfectly and I believe open with the gas flow so some gasses would probably seep by, especially under full boost...but the egr cooler might get heat soaked with the constant gas pressure fed to it going nowhere. I dunno
I'm not sure how not running the plate would affect things if you're running a tune that shut the egr off tho, I'm by no means an expert. Do you have tuning and have you deleted the DPF?
I'd imagine having tuning shutting the egr off and not running the blocker plate while running the DPF, your DPF will accumulate soot faster and regen more frequently and yield poor fuel economy tho.
Again I'm no expert and, having the LBZ I really haven't familiarized myself with the emissions components that the LMM has as the LBZ doesn't have all the emissions the LMM has.
You don't need any special tools to do this mod, ratcheting box ends make quick work of most jobs and help to have.
You can do this
just plan on it taking a few hours and don't give up, I used to think these trucks were super complicated and insanely difficult to work on, but as it turns out most everything is pretty simple, it's just "layered work" there always seems to be one if not several things that needs to be removed to get to what ya want and everything is really tight so patience and creative thinking is a must